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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOPEPTIDASE ERAP2 WITH LIGAND
 
Authors :  A. Mpakali, P. Giastas, E. Saridakis, I. M. Mavridis, E. Stratikos
Date :  31 Jul 15  (Deposition) - 30 Sep 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Aminopeptidase, Erap2, Zinc Ion Binding, Endoplasmic Reticulum, Hydrolase, Metalloprotease, L-Rap, Antigen Presentation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Mpakali, P. Giastas, N. Mathioudakis, I. M. Mavridis, E. Saridakis E. Stratikos
Structural Basis For Antigenic Peptide Recognition And Processing By Endoplasmic Reticulum (Er) Aminopeptidase 2.
J. Biol. Chem. V. 290 26021 2015
PubMed-ID: 26381406  |  Reference-DOI: 10.1074/JBC.M115.685909

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2
    Chains: A, B
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LEUKOCYTE-DERIVED ARGININE AMINOPEPTIDASE, L-RAP
 
Molecule 2 - GPI
    Chains: C, D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 37)

Asymmetric Unit (4, 37)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3NAG25Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 21)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:370 , HIS A:374 , GLU A:393 , GLY C:1 , PRO C:2BINDING SITE FOR RESIDUE ZN A1119
02AC2SOFTWARETYR A:313 , HOH A:2039BINDING SITE FOR RESIDUE EDO A1962
03AC3SOFTWARELYS A:476BINDING SITE FOR RESIDUE EDO A1963
04AC4SOFTWAREHIS B:370 , HIS B:374 , GLU B:393 , GLY D:1 , PRO D:2BINDING SITE FOR RESIDUE ZN B1119
05AC5SOFTWAREMET B:778BINDING SITE FOR RESIDUE EDO B1962
06AC6SOFTWAREGLN B:776BINDING SITE FOR RESIDUE EDO B1963
07AC7SOFTWAREHIS A:83 , ASN A:85 , GLU A:227 , LEU A:248 , HOH A:2075 , ARG B:293BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1001 THROUGH BMA A1003 BOUND TO ASN A 85
08AC8SOFTWAREASN A:103BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1012 THROUGH NAG A1013 BOUND TO ASN A 103
09AC9SOFTWAREASN A:119 , ASP A:167BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1004 THROUGH NAG A1005 BOUND TO ASN A 119
10BC1SOFTWAREASN A:219 , THR A:255 , VAL A:257 , LYS A:258 , TYR A:487BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1006 THROUGH BMA A1008 BOUND TO ASN A 219
11BC2SOFTWAREASN A:294BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1016 THROUGH NAG A1017 BOUND TO ASN A 294
12BC3SOFTWAREASN A:405 , HOH A:2079BINDING SITE FOR MONO-SACCHARIDE NAG A1009 BOUND TO ASN A 405
13BC4SOFTWAREASN A:431 , LYS A:545BINDING SITE FOR MONO-SACCHARIDE NAG A1018 BOUND TO ASN A 431
14BC5SOFTWAREASN A:650 , HOH A:2080 , HOH A:2081BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1010 THROUGH NAG A1011 BOUND TO ASN A 650
15BC6SOFTWAREASN A:714BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1014 THROUGH NAG A1015 BOUND TO ASN A 714
16BC7SOFTWAREHIS A:272 , SER A:273 , ASP A:291 , ARG A:293 , ASN B:85 , SER B:88 , GLU B:227 , LEU B:248 , HOH B:2001 , HOH B:2020BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1001 THROUGH BMA B1004 BOUND TO ASN B 85
17BC8SOFTWAREASN B:103BINDING SITE FOR MONO-SACCHARIDE NAG B1005 BOUND TO ASN B 103
18BC9SOFTWAREASN B:219 , THR B:255 , LYS B:258BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1008 THROUGH NAG B1009 BOUND TO ASN B 219
19CC1SOFTWAREASN B:405 , LYS B:466 , GLU B:471BINDING SITE FOR MONO-SACCHARIDE NAG B1010 BOUND TO ASN B 405
20CC2SOFTWAREASN B:431 , LYS B:545BINDING SITE FOR MONO-SACCHARIDE NAG B1011 BOUND TO ASN B 431
21CC3SOFTWAREASN B:650BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1006 THROUGH NAG B1007 BOUND TO ASN B 650

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:421 -A:460
2A:759 -A:766
3B:421 -B:460
4B:759 -B:766

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Lys A:132 -Pro A:133
2Gly A:134 -Lys A:135
3Glu A:200 -Pro A:201
4Thr B:57 -Asn B:58
5Gly B:59 -Glu B:60
6Lys B:132 -Pro B:133
7Glu B:200 -Pro B:201
8Asp B:574 -Pro B:575
9Leu B:614 -Pro B:615
10Gln B:649 -Asn B:650
11Leu B:889 -Gly B:890
12Gly B:925 -Ser B:926
13Pro C:2 -Gly C:3
14Arg C:4 -Ala C:5
15Gly D:1 -Pro D:2
16Pro D:2 -Gly D:3

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AB2)

(-) Exons   (0, 0)

(no "Exon" information available for 5AB2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:897
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeeeeee....eeeeeeeeeeee.....eeeee....eeeeee.....hhhhh......eeeeehhh.eeeee.........eeeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeeeee.....eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee......ee....eeeeehhhhh......hhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh...eeeeeee...eeee.eee..........hhhhhh......eeeeeee......eeeee....eeee.......eee.hhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ab2 A  54 PVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDSRYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLKEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSHSDPKMTSNMLAFLGENAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQEDPEWRALQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTRH 962
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          502|                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           515                                                                                                                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:879
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeeeeeeeee....eeeeeeeeeee.......eeee....eeeeeeeee.............eeeee....eeeee..........eeeeeeeeee......eeeeeeee.....eeeeeeee....hhhhh...........eeeeeeee....eeee...eeee.......eeeee......hhhhh.eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee......ee....eeeee.hhh.......hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhh........hhhhhhhh......eeeeee......eeeeee.........................ee........ee.....................hhhhh...eeee......hhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ab2 B  54 PVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDSRYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLKEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQEDPEWRALQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTR 961
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          502|                                                                                                                                                                                                                                                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           532                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5ab2 C   1 GPGRAF   6


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5ab2 D   1 GPGRAF   6
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5AB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AB2)

(-) Gene Ontology  (22, 22)

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  Cis Peptide Bonds
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        ERAP2_HUMAN | Q6P179: 3se6 4e36 4jbs 5ab0 5cu5 5j6s 5k1v

(-) Related Entries Specified in the PDB File

5ab0 CRYSTAL STRUCTURE OF AMINOPEPTIDASE ERAP2 WITH LIGAND